Questions
Allowing multi-threading with up to 4 threads. [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..."
| Wald padj < 0.05 | LFC > 0 (Wald padj < 0.05) | LFC < 0 (Wald padj < 0.05) | |
|---|---|---|---|
| GF VS SPF (F, 8w) | 392 | 192 | 200 |
| GF VS SPF (M, 8w) | 161 | 76 | 85 |
| GF VS SPF (F, 52w) | 738 | 316 | 422 |
| GF VS SPF (M, 52w) | 393 | 145 | 248 |
| GF VS SPF (F, 104w) | 2038 | 846 | 1192 |
| GF VS SPF (M, 104w) | 2172 | 898 | 1274 |
GF VS SPF (F, 8w) GF VS SPF (M, 8w) GF VS SPF (F, 52w) GF VS SPF (M, 52w)
0.5790816 0.6832298 0.4363144 0.6030534
GF VS SPF (F, 104w) GF VS SPF (M, 104w)
0.5662414 0.5382136
Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in stack.default(getgo(rownames(l$deg), "mm10", "geneSymbol")): “non-vector elements will be ignored”Warning message in stack.default(getgo(rownames(as.data.frame(l$deg)), "mm10", "geneSymbol", : “non-vector elements will be ignored”
Warning message: “Removed 14812 rows containing non-finite values (stat_density).”
Differentially expressed genes
| GF vs SPF | 8w | 52w | 104w |
|---|---|---|---|
| F | |||
| M |
Dot-plot with the 20 most significant p-values for the different comparison
Using term, id as id variables Using term, id as id variables
Network based on description similarity
| GF vs SPF | 8w | 52w | 104w |
|---|---|---|---|
| F | |||
| M |
GF VS SPF (F, 8w)
GF VS SPF (M, 8w)
GF VS SPF (F, 52w)
GF VS SPF (M, 52w)
GF VS SPF (F, 104w)
GF VS SPF (M, 104w)
Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)
Using term, id as id variables Using term, id as id variables
Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)
Using term, id as id variables Using term, id as id variables
[1] "Note: 5 of 3451 unique input IDs unmapped." [1] "Note: 5 of 3451 unique input IDs unmapped."
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Pathway graphs available at ../results/dge/type-effect/type_gender_age/over_repr_kegg/
[1] "Note: 5 of 3451 unique input IDs unmapped."
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[1] "Note: 5 of 3451 unique input IDs unmapped." [1] "Note: 5 of 3451 unique input IDs unmapped." [1] "Note: 5 of 3451 unique input IDs unmapped."
Pathway graphs available at ../results/dge/type-effect/type_gender_age/under_repr_kegg/
Protocol: 2 months old female mices (GF vs SPF)
| Symbols | Genes | fold.d.h | GF_1 | GF_2 | GF_3 | GF_4 | GF_5 | GF_7 | GF_8 | SPF_1 | SPF_2 | SPF_3 | SPF_4 | SPF_6 | SPF_7 | SPF_8 | t.test |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ddit4 | NM_029083 | 3.488386 | 232 | 420 | 140 | 116 | 1027 | 785 | 501 | 40 | 21 | 22 | 13 | 73 | 70 | 48 | 0.007198903 |
| Iqgap1 | NM_016721 | 2.545650 | 24 | 44 | 10 | 16 | 20 | 17 | 50 | 4 | 14 | 2 | 3 | 1 | 6 | 1 | 0.003764139 |
| Tsc22d3 | NM_001077364 | 2.416164 | 47 | 107 | 44 | 53 | 257 | 214 | 132 | 23 | 17 | 23 | 20 | 39 | 16 | 22 | 0.009737505 |
| Rab3d | NM_031874 | 2.369234 | 7 | 14 | 5 | 10 | 2 | 7 | 17 | 1 | 1 | 1 | 1 | 3 | 1 | 4 | 0.004171454 |
| Gnaz | NM_010311 | 2.280108 | 1 | 1 | 5 | 5 | 9 | 9 | 4 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.009123198 |
| Agpat4 | NM_026644 | 1.984893 | 5 | 21 | 21 | 10 | 15 | 10 | 13 | 4 | 7 | 1 | 1 | 5 | 5 | 1 | 0.001279054 |
| erny | our | |
|---|---|---|
| Ddit4 | 3.4883860 | 3.6294025 |
| Tsc22d3 | 2.4161642 | 1.4193018 |
| Notch4 | 1.4226911 | 1.6315226 |
| Sult1a1 | 1.2561528 | 1.1617315 |
| Capg | 0.9126729 | 0.5168264 |
| Ucp2 | 0.9111967 | 0.5044607 |
| Gpr137b | 0.8032544 | 1.2266600 |
| Pnpla2 | 0.7100179 | 0.4259134 |
| Ogfrl1 | 0.6877922 | 0.6959325 |
| Arhgef6 | -1.0246621 | 0.4253851 |
| Gpr137b-ps | -1.1178365 | -3.0251734 |
| Upk1b | -1.1300605 | -0.6517569 |
| Cntrl | -1.3303078 | -0.9347969 |
| Apobec2 | -1.4288433 | -0.8472098 |
| Ly86 | -1.4389640 | -0.9562232 |
| Stard3nl | -1.4780473 | -0.4310033 |
| Fkbp7 | -1.6261852 | -0.3942576 |
| Malat1 | -1.7120031 | -1.1023659 |
| Mcur1 | -1.7424200 | -0.8593199 |
| Nos1ap | -1.8022360 | -0.8171791 |
| Zfp318 | -1.8961642 | -0.7895965 |
| Lrba | -2.0198996 | -0.6372855 |
| Far1 | -2.5766472 | 0.5588240 |
| Ero1lb | -3.2172307 | -1.3952799 |
Error in counts[, SPF_F_8w_samples]: object of type 'closure' is not subsettable Traceback: